Objectives

  • Use catalogueR to query all 110 datasets in the eQTL Catalogue for eQTLs that overlap with COVID-19 GWAS-nominated SNPs.
  • Identify which tissues, cell-types, and genes may be most relevant for genetic COVID-19 susceptibility.

Import and prepare SNPs

Since catalogueR expects a list of files with per-Locus summary stats, we’ll just save each SNP as its own “locus” file.

Summarise

Annotate tissues using metadata

Count the number of unique SNPs, eQTL genes, significant eGenes per tissue/cell-type.

Note: eQTL Catalogue only provides raw p-values, so you’ll need to infer your own signficance correction threshold. For simplicity, I use p < 5e-8 here.

## `summarise()` regrouping output by 'System', 'Tissue_group' (override with `.groups` argument)